Validation of the use of whole-genome amplified DNA in a population-based study

验证全基因组扩增 DNA 在基于人群的研究中的使用

• 批准号: 8445608
• 负责人: IRENE ORLOW
• 金额: $ 8.53万
• 依托单位: SLOAN-KETTERING INST CAN RESEARCH
• 依托单位国家: 美国
• 财政年份: 2013
• 资助国家: 美国
• 起止时间: 2013-01-02 至 2014-11-30
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/8445608
• 关键词: Address; Alleles; Blood; CDKN2A gene; Candidate Disease Gene; Characteristics; DNA; DNA amplification; Data; Epidemiologic Studies; Epidemiology; Family history of; Foundations; Funding; Future; Genes; Genetic; Genetic Polymorphism; Genome; Genotype; Germ-Line Mutation; Goals; Health; Histopathology; Incidence; Investigation; Knowledge; Link; Malignant Neoplasms; Methods; Molecular; Mutation; Pathway interactions; Performance; Prevention; Productivity; Public Health; Publishing; Questionnaires; Reporting; Reproducibility; Research; Research Personnel; Resources; Risk; SNP genotyping; Sampling; Sensitivity and Specificity; Somatic Mutation; Source; Sun Exposure; Techniques; Technology; Testing; Tumor Immunity; Validation; Variant; abstracting; base; cost; interest; melanoma; population based; screening; tumor; tumor progression; validation studies

DESCRIPTION (provided by applicant): Abstract Whole-genome amplification (WGA) technologies offer the opportunity to expand DNA from otherwise depleted native DNAs. This technique has the potential to facilitate the continued productivity of molecular epidemiological studies that have limited remaining DNA. Although allele amplification errors can occur, the performance of WGA in SNP genotyping has generally reported very good concordance and reproducibility. However the quality of WGA DNA obtained from buccal brushes has not been thoroughly evaluated for screening of mutations or sequencing, and published reports have mostly involved limited sets of DNA samples extracted from other sources and tested for the fidelity of non- PCR based WGA methods. The objective of this validation study is to determine the sensitivity and specificity of detecting germline mutations and polymorphisms in a large set of WGA DNA samples from a population-based study by direct sequencing. We plan to sequence the CDKN2A/p16 gene in 3580 DNA samples from buccal brushes that has been whole-genome amplified with the GenomePlex(R) kit, and then compare the sequencing data with those results already obtained in the original or native DNAs. We endeavor to demonstrate that we can use the WGA random fragmentation- PCR method to allow nearly unlimited future studies of germline DNA using this resource to investigate hypotheses in relation to melanoma risk and/or progression. The study also has a broader scientific relevance in that it will provide generalizable knowledge about the utility of buccal samples for future epidemiological investigations.

描述（由申请人提供）：摘要全基因组扩增（WGA）技术提供了从原本耗尽的天然DNA扩增DNA的机会。这种技术有可能促进剩余DNA有限的分子流行病学研究的持续生产力。虽然可能发生等位基因扩增错误，但WGA在SNP基因分型中的表现通常具有非常好的一致性和再现性。然而，从口腔刷获得的WGA DNA的质量尚未被彻底评估用于突变筛选或测序，并且已发表的报道大多涉及从其他来源提取的有限组的DNA样品，并测试了基于非PCR的WGA方法的保真度。本验证研究的目的是通过直接测序确定检测来自基于人群研究的大量WGA DNA样本中生殖系突变和多态性的灵敏度和特异性。我们计划对3580份已用Genomeplasmid（R）试剂盒进行全基因组扩增的口腔刷DNA样品中的CDKN 2A/p16基因进行测序，然后将测序数据与原始或天然DNA中已经获得的结果进行比较。我们奋进证明，我们可以使用WGA随机片段化- PCR方法，以允许几乎无限的生殖系DNA的未来研究，使用此资源来调查与黑色素瘤风险和/或进展有关的假设。该研究还具有更广泛的科学相关性，因为它将为未来的流行病学调查提供有关口腔样本效用的可推广知识。